Pjotr Prins

This study evaluates the impact of an individual-specific pangenome on somatic variant calling in a pediatric AML patient, finding reduced false positives and altered phylogenetic branching.

The paper benchmarks frontier and local LLMs on a biomedical knowledge graph using expert-curated questions and a new evaluation metric called psi.

This study identifies genetic loci affecting lifespan dynamics, sex differences, and body weight trade-offs in mice using an actuarial approach.

This paper introduces adaptive tracepoints for compressing pangenome alignments, achieving significant compression ratios while maintaining alignment accuracy.

This paper introduces pangenome-informed language models for generating synthetic DNA sequences, showing improved efficiency and quality over classical methods.

GNQA, a retrieval-augmented GPT question-answering system over 3000 GeneNetwork, aging and diabetes papers, cites source paragraphs; RAGAS rated answer relevance above human thumbs-up ratings (89% vs 76%).

This study investigates the long-term epigenetic effects of Gulf War illness by analyzing DNA methylation in mice exposed to stress and organophosphate compounds.

This paper uses IBD-based clustering to reveal environmental and health disparities across subcommunities in a biobank dataset.

This study quantifies protein expression in rat brains, identifies pQTLs, and links them to behavioral traits and human disorders.

This study constructs a rat pangenome from linked-read data to enhance variant discovery and genotype-phenotype mapping in recombinant inbred strains.

The paper analyzes genomic data from a diverse cohort to highlight genetic diversity and disparities in disease prevalence linked to ancestry and environment.

This paper introduces PGGB, a pipeline for building pangenome graphs that includes all variation without bias, enabling variation detection, conservation measurement, recombination event detection, and phylogenetic inference.

The paper introduces nf-core/pangenome, a scalable and reference-unbiased pipeline for constructing pangenome graphs, achieving faster performance than PGGB on large datasets.

The paper presents an improved rat reference genome, mRatBN7.2, which enhances genomic, transcriptomic, and proteomics data mapping and identifies millions of genetic variations across rat strains.

This paper introduces a graph layout algorithm for pangenome graphs, enabling efficient visualization of large-scale genomic data.

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

ODGI is a tool suite for analyzing pangenome graphs, enabling efficient exploration and manipulation of large-scale genomic data.

This study uses LMM-MQM time series mapping to identify additional QTLs for body weight in mice, improving the explained variance of a known locus and detecting novel loci.

The paper develops GPU-accelerated algorithms for fast eQTL scans in BXD mice, reducing runtime to seconds for large transcriptome datasets.

The paper quantifies heritability of THC responses in BXD mice strains and identifies candidate genes associated with variation in initial sensitivity to THC effects.

A C++ library plus 83 command line utilities and 44 scripts (vcflib) for filtering, transforming and computing population-genetic statistics on VCF files, with companion tools bio-vcf, slivar, cyvcf2 and hts-nim.

The paper shows that conserved codon usage in highly expressed genes correlates with reduced mRNA secondary structure variability, enhancing translation efficiency and mRNA stability.

GeneCup mines PubMed for gene relationships using a custom ontology and deep learning to organize and present relevant literature and GWAS results.

This paper introduces a homomorphic encryption method for genotypes and phenotypes to enable privacy-preserving quantitative genetic analysis across studies.

BXD mouse family doubled to 150 inbred strains segregating over 6 million variants, with roughly 10,000 located recombinations and a public phenome exceeding 7000 traits.

R/qtl2 is a software tool for QTL mapping in multi-parent populations and high-dimensional data, offering features like linear mixed models and SNP imputation.